ns_heatmap: Create a heatmap from clustered tandem repeat squiggles.

In arnederoeck/NanoSatelliteR: QC, plotting, and clustering of tandem repeat segmentation created by NanoSatellite.

Description

This function writes a png figure containing a heatmap based on a distance matrix of clustered tandem repeat squiggle units.

Usage

ns_heatmap(distmat, file, lwd = 10, max_dist = NA, rm0 = F)

Arguments

distmat	A distance matrix, generated by dtwclust::tsclust()
file	A character of length 1 containing path and name of the file.
lwd	Dendrogram line width
max_dist	Remove distances higher than this numeric value (to obtain a graphically relevant color scale)
rm0	A logical indicating wether distance equal to zero should be removed (to obtain a graphically relevant color scale)

Details

To visually inspect clustering, a heatmap can be constructed. Due to the potential large distance matrices generated by dtwclust::tsclust(), creating heatmaps can be troublesome. ns_heatmap() should be able to deal with large distance matrices. Distances in the resulting heatmap are shown with a color scale: Black = low distance, white = medium distance, red = high distance. In addition, this function provides a few parameters to change thickness of dendrograms and remove extreme distances.

Examples

df <- load_summary("/storage/NanoSatellite_chunks/")
qc <- summary_qc(df)
df2 <- qual_reads(df,qc$center_cutoff)
squiggles <- load_squiggles("/storage/NanoSatellite_chunks/",df2)

library(doParallel)
library(dtwclust)
k_clusters=2
registerDoParallel(cores=8)

positive_clustering=tsclust(squiggles$positive,type="h",k=k_clusters,trace=TRUE,distance = "dtw_basic", control=hierarchical_control(method="ward.D",symmetric = T))
ns_heatmap(positive_clustering@distmat,"~/test.png",max_dist=200,rm0=T)

arnederoeck/NanoSatelliteR documentation built on May 6, 2019, 1:35 a.m.